Please be patient with these questions since I have no personal experience to reference.
What should have been the final destination of these documents? Should they have become part of Bush's file? And why the hard-nosed attitude? Hadn't Bush been completing his hours at a better than average pace (I really don't understand what the requirements were but since I read he accumulated enough points to have served 15 years I'm assuming his hours were better than average), and scoring well on tests?
These document purport to show an officer that had disobeyed a "direct order" to take his flight physical. Now, as GW's commanding officer that memo should have been carbon copied to all involved up the chain of command plus GW's own personnel file. We can see that no one was copied, no copies from Bush's pentagon files are include his copy. This "commanding officer" either put his own career and credibility on the line by suppressing the memo OR he didn't write the damn things.